gsHeatmap: A function to create a simple heatmap and key.

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

A function to create a simple heatmap and key.

Description

This is an internal function called by runRomer and is not intended to be used directly. It is documented here only because arguments may be passed down via the dots argument.

Usage

gsHeatmap(
  object,
  ind,
  filename,
  columns = NULL,
  colnames = NULL,
  col = NULL,
  annot = NULL,
  scale.row = FALSE,
  key = TRUE,
  bline = NULL
)

Arguments

object	An ExpressionSet containing normalized, summarized gene expression data.
ind	Numeric vector indicating which rows of the ExpressionSet to use.
filename	The filename for the heatmap and associated key.
columns	Numeric vector indicating which columns of the ExpressionSet to use. If NULL, all columns will be used.
colnames	Character. Substitute column names for the heatmap. If NULL, the sampleNames will be used.
col	A vector of colors to use for the heatmap. If NULL, the bluered function will be used.
annot	A matrix or data.frame containing gene symbols to annotate the heatmap. This will normally be extracted automatically from the 'fit' object passed to geneSetPage. If there is no annotation in the fit object, then the probe IDs will be used instead.
scale.row	Boolean. Should the data be scaled by row? Defaults to FALSE.
key	Boolean. Should a key be produced that shows the numeric range for the colors of the heatmap? Defaults to TRUE.
bline	A numeric vector, usually extracted from a contrast matrix, used to ‘sweep’ the mean baseline sample means from the heatmap data. The end result will be a heatmap in which the colors correspond to log fold changes from the baseline samples.

Details

As noted above, this is only intended to be called indirectly by runRomer. However, certain arguments such as scale.row, or col, etc, can be passed down to this function via the dots argument, allowing the end user to have more control over the finished product.

Value

Nothing is returned. Called only for the side effect of creating heatmaps in 'png' format.

Author(s)

James W. MacDonald <[e-mail]>

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.